Margaret married Philip III of Spain, her first cousin, once-removed, on 18 April 1599 and became a very influential figure at her husband's court. Philip had an "affectionate, close relationship" with Margaret, and paid her additional attention after she bore him a son in 1605.[1]

Margaret was also a great patroness of the arts. She was considered by contemporaries[who?] to be a very pious Catholic and "astute and very skillful" in her political dealings.[2]

Alongside the Empress Maria, widow of Holy Roman EmperorMaximilian II, and the latter's daughter Archduchess Margaret, who lived as a nun in Madrid, Queen Margaret formed a circle of women wielding considerable influence over the king.[3] They emphasised Spain's status as a Catholic power acting in the interest of Catholic Europe and also highlighted the unity of the House of Habsburg.[3] They were successful, for example, in convincing Philip to provide financial support to Holy Roman Emperor Ferdinand II.[1]

The pro-Austrian camp at the Spanish court was opposed by the Duke of Lerma, the King's chief minister, who argued that Spain should pursue her own course of action independently of religious or dynastic ties. Queen Margaret was "melancholic" and unhappy about the influence of Duke, whom she considered corrupt, over her husband,[2] and continually fought him for influence over the king. In this conflict, she was supported by her favourite Mariana de San José, prioress of the Monasteria la Encarnación, her husband's confessor Father Luis de Aliaga, and her daughter Maria Anna's confessor, the Franciscan friar Juan de Santa María - who was felt by contemporaries[who?] to have an excessive influence over the King at the end of his life.[4] The Duke of Lerma was eventually removed from power in 1618, though only after Margaret's death.

Margaret died while giving birth to her youngest child, Alfonso. Her husband never remarried and died ten years later.